MolNFT v1 · #121513 · protein
Structure-function analysis of functionally diverse members of the cyclic amide hydrolase family of toblerone fold enzymes
5HXU · Barbiturase: “Structure-function analysis of functionally diverse members of the cyclic amide hydrolase family of toblerone…”. X-ray diffraction, 4 ligands (MHA, NA, SO4), 7 pockets (best druggability 0.66). MolNFT v1 #121513 on…
- PDB
- 5HXU
- Type
- protein
- Length
- 734 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Barbiturase
- EC
- 3.5.2.1
- UniProt
- Q8RSQ2
- Ligands
- MHA, NA, SO4, CL
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Barbiturase (EC 3.5.2.1) | protein | 367 | 32% helix, 26% strand | Q8RSQ2 |
| B | Barbiturase (EC 3.5.2.1) | protein | 367 | 33% helix, 27% strand | Q8RSQ2 |
Ligands and binding sites
- MHA · (carbamoylmethyl-carboxymethyl-amino)-acetic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.66 | 0.96 | 20 | MHA |
| 2 | 120 | 0.62 | 0.87 | 23 | empty |
| 3 | 167 | 0.54 | 0.80 | 30 | empty |
| 4 | 170 | 0.52 | 0.79 | 25 | empty |
| 5 | 75 | 0.36 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1815 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5HXU · Structure-function analysis of functionally diverse members of the cyclic amide hydrolase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8RSQ2 · AlphaFold monomer V2.0 prediction for barbiturase (Q8RSQ2) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q8RSQ2
- Elsewhere: RCSB PDB 5HXU · PDBe 5HXU · UniProt Q8RSQ2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.